Gene Expression and Transcript Profiling, Direct Analysis, Indirect, Nucleic Acid, Nucleotide, Parallel Signature

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Home >> Plant Biotechnology and Genomics >>Whole Genome Sequencing and Functional Genomics >> Gene Expression and Transcript Profiling

	Gene expression and transcript profiling Gene expression studies through transcript profiling are an important area of research in the field of functional genomics. In contrast to gene finding methods, where one gene is studied at a time, expression profiles allow analysis of the whole genome at the same time. A number of methods are available for transcript profiling. These methods can be divided into two groups (i) Direct analysis involving either the nucleotide sequencing of cDNAs or the analysis of fragments of different sizes; (ii) Indirect analysis, involving nucleic acid, hybridization of mRNA or cDNA fragments.
Direct analysis Direct analysis by nucleotide sequencing includes the following methods (i) large scale EST sequencing, (ii) serial analysis of gene expression (SAGE); (iii) massively parallel signature sequencing (MPSS). The other methods involving direct analysis of the fragments of different sizes are also available and include the following techniques. (i) differential display (ii) selective amplification of fragments derived from cDNA. These techniques are discussed elsewhere in different chapters of the book and therefore will not be discussed here.
Indirect analysis High throughput analysis of expression profiles involves nucleic acid hybridization utilizing DNA chips and microarrays. These methods make use of either (i) the oligonucleotides based arrays or (ii) cDNA microarrays. Several laboratories have generated Arabidopsisspecific microarrays. At least two publicly funded programs are also available, which provide world-wide microarray services. These include AGFC i.e. ArabidopsisFunctional Genomics Consortium (funded by NSF, USA) and the other is GARNet in UK. Other microarray resources for Arabidopsis include.
Stanford Microarray Database (SMD), (ii) The Arabidopsis Information Resource (TAIR); (iii) The Institute of Genome Research (TIGR); (iv) Moanto; (v) Affymetrix and (vi) Synteny/InCyte. Novartis Agricultural Discovery Institute or NADI (San Diego, California) also designed an oligonucleotide microarray containing probes from more than 8000 genes, -300 of them with unknown functions. Utilizing this microarray more than 500 Arabidopsis transcription profiles were produced by the year 2000. These profiles describe the gene expression patterns in different organs/tissues and in different growth environments. The Arabidopsis transcription profiles proved to be valuable in gene discovery and in the characterization of regulatory pathways. Similar studies in several crops including rice are being initiated in several laboratories around the world.

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